diff --git a/.github/workflows/software/bwa_index.yml b/.github/workflows/software/bwa_index.yml index 7a045703..a2cfe096 100644 --- a/.github/workflows/software/bwa_index.yml +++ b/.github/workflows/software/bwa_index.yml @@ -3,13 +3,13 @@ on: push: paths: - software/bwa/index/** - - .github/workflows/bwa_index.yml - - tests + - .github/workflows/software/bwa_index.yml + - tests/software/bwa/** pull_request: paths: - software/bwa/index/** - - .github/workflows/bwa_index.yml - - tests + - .github/workflows/software/bwa_index.yml + - tests/software/bwa/** jobs: ci_test: diff --git a/.github/workflows/software/bwa_mem.yml b/.github/workflows/software/bwa_mem.yml index 20c438f6..581f8c3d 100644 --- a/.github/workflows/software/bwa_mem.yml +++ b/.github/workflows/software/bwa_mem.yml @@ -3,13 +3,13 @@ on: push: paths: - software/bwa/mem/** - - .github/workflows/bwa_mem.yml - - tests + - .github/workflows/software/bwa_mem.yml + - tests/software/bwa/** pull_request: paths: - software/bwa/mem/** - - .github/workflows/bwa_mem.yml - - tests + - .github/workflows/software/bwa_mem.yml + - tests/software/bwa/** jobs: ci_test: diff --git a/.github/workflows/software/fastqc.yml b/.github/workflows/software/fastqc.yml index 1379b8bb..9e38f1f5 100644 --- a/.github/workflows/software/fastqc.yml +++ b/.github/workflows/software/fastqc.yml @@ -3,13 +3,13 @@ on: push: paths: - software/fastqc/** - - .github/workflows/fastqc.yml - - tests + - .github/workflows/software/fastqc.yml + - tests/software/fastqc/** pull_request: paths: - software/fastqc/** - - .github/workflows/fastqc.yml - - tests + - .github/workflows/software/fastqc.yml + - tests/software/fastqc/** jobs: ci_test: @@ -17,21 +17,20 @@ jobs: env: NXF_ANSI_LOG: false steps: + - uses: actions/checkout@v2 - - uses: actions/checkout@v2 + - name: Install Nextflow + run: | + export NXF_VER="20.07.1" + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ - - name: Install Nextflow - run: | - export NXF_VER="20.07.1" - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: "3.x" - - name: Install dependencies - run: python -m pip install --upgrade pip pytest-workflow - - # Test the module - - run: pytest --tag fastqc --symlink --wt 2 + # Test the module + - run: pytest --tag fastqc --symlink --wt 2 diff --git a/.github/workflows/software/picard_collectmultiplemetrics.yml b/.github/workflows/software/picard_collectmultiplemetrics.yml index 4c6576f4..6c85840d 100644 --- a/.github/workflows/software/picard_collectmultiplemetrics.yml +++ b/.github/workflows/software/picard_collectmultiplemetrics.yml @@ -3,13 +3,13 @@ on: push: paths: - software/picard/collectmultiplemetrics/** - - .github/workflows/picard_collectmultiplemetrics.yml - - tests + - .github/workflows/software/picard_collectmultiplemetrics.yml + - tests/software/picard/** pull_request: paths: - software/picard/collectmultiplemetrics/** - - .github/workflows/picard_collectmultiplemetrics.yml - - tests + - .github/workflows/software/picard_collectmultiplemetrics.yml + - tests/software/picard/** jobs: ci_test: diff --git a/.github/workflows/software/picard_markduplicates.yml b/.github/workflows/software/picard_markduplicates.yml index fe4814be..186bbac9 100644 --- a/.github/workflows/software/picard_markduplicates.yml +++ b/.github/workflows/software/picard_markduplicates.yml @@ -3,13 +3,13 @@ on: push: paths: - software/picard/markduplicates/** - - .github/workflows/picard_markduplicates.yml - - tests + - .github/workflows/software/picard_markduplicates.yml + - tests/software/picard/** pull_request: paths: - software/picard/markduplicates/** - - .github/workflows/picard_markduplicates.yml - - tests + - .github/workflows/software/picard_markduplicates.yml + - tests/software/picard/** jobs: ci_test: diff --git a/.github/workflows/software/picard_mergesamfiles.yml b/.github/workflows/software/picard_mergesamfiles.yml index 6798822a..c67e5d42 100644 --- a/.github/workflows/software/picard_mergesamfiles.yml +++ b/.github/workflows/software/picard_mergesamfiles.yml @@ -3,13 +3,13 @@ on: push: paths: - software/picard/mergesamfiles/** - - .github/workflows/picard_mergesamfiles.yml - - tests + - .github/workflows/software/picard_mergesamfiles.yml + - tests/software/picard/** pull_request: paths: - software/picard/mergesamfiles/** - - .github/workflows/picard_mergesamfiles.yml - - tests + - .github/workflows/software/picard_mergesamfiles.yml + - tests/software/picard/** jobs: ci_test: diff --git a/.github/workflows/software/samtools_flagstat.yml b/.github/workflows/software/samtools_flagstat.yml index 6ade3ee8..2946dfc6 100644 --- a/.github/workflows/software/samtools_flagstat.yml +++ b/.github/workflows/software/samtools_flagstat.yml @@ -3,13 +3,13 @@ on: push: paths: - software/samtools/flagstat/** - - .github/workflows/samtools_flagstat.yml - - tests + - .github/workflows/software/samtools_flagstat.yml + - tests/software/samtools/** pull_request: paths: - software/samtools/flagstat/** - - .github/workflows/samtools_flagstat.yml - - tests + - .github/workflows/software/samtools_flagstat.yml + - tests/software/samtools/** jobs: ci_test: diff --git a/.github/workflows/software/samtools_idxstats.yml b/.github/workflows/software/samtools_idxstats.yml index efc67e32..c55b7f43 100644 --- a/.github/workflows/software/samtools_idxstats.yml +++ b/.github/workflows/software/samtools_idxstats.yml @@ -3,13 +3,13 @@ on: push: paths: - software/samtools/idxstats/** - - .github/workflows/samtools_idxstats.yml - - tests + - .github/workflows/software/samtools_idxstats.yml + - tests/software/samtools/** pull_request: paths: - software/samtools/idxstats/** - - .github/workflows/samtools_idxstats.yml - - tests + - .github/workflows/software/samtools_idxstats.yml + - tests/software/samtools/** jobs: ci_test: diff --git a/.github/workflows/software/samtools_index.yml b/.github/workflows/software/samtools_index.yml index 2a1ed2d5..9ae9a711 100644 --- a/.github/workflows/software/samtools_index.yml +++ b/.github/workflows/software/samtools_index.yml @@ -3,13 +3,13 @@ on: push: paths: - software/samtools/index/** - - .github/workflows/samtools_index.yml - - tests + - .github/workflows/software/samtools_index.yml + - tests/software/samtools/** pull_request: paths: - software/samtools/index/** - - .github/workflows/samtools_index.yml - - tests + - .github/workflows/software/samtools_index.yml + - tests/software/samtools/** jobs: ci_test: diff --git a/.github/workflows/software/samtools_sort.yml b/.github/workflows/software/samtools_sort.yml index a090fcdf..6edf64f7 100644 --- a/.github/workflows/software/samtools_sort.yml +++ b/.github/workflows/software/samtools_sort.yml @@ -3,13 +3,13 @@ on: push: paths: - software/samtools/sort/** - - .github/workflows/samtools_sort.yml - - tests + - .github/workflows/software/samtools_sort.yml + - tests/software/samtools/** pull_request: paths: - software/samtools/sort/** - - .github/workflows/samtools_sort.yml - - tests + - .github/workflows/software/samtools_sort.yml + - tests/software/samtools/** jobs: ci_test: diff --git a/.github/workflows/software/samtools_stats.yml b/.github/workflows/software/samtools_stats.yml index cbc9e7b3..d00b1ff3 100644 --- a/.github/workflows/software/samtools_stats.yml +++ b/.github/workflows/software/samtools_stats.yml @@ -3,13 +3,13 @@ on: push: paths: - software/samtools/stats/** - - .github/workflows/samtools_stats.yml - - tests + - .github/workflows/software/software/samtools_stats.yml + - tests/software/samtools/** pull_request: paths: - software/samtools/stats/** - - .github/workflows/samtools_stats.yml - - tests + - .github/workflows/software/software/samtools_stats.yml + - tests/software/samtools/** jobs: ci_test: diff --git a/.github/workflows/software/trimgalore.yml b/.github/workflows/software/trimgalore.yml index 16081569..b4f09918 100644 --- a/.github/workflows/software/trimgalore.yml +++ b/.github/workflows/software/trimgalore.yml @@ -3,13 +3,13 @@ on: push: paths: - software/trimgalore/** - - .github/workflows/trimgalore.yml - - tests + - .github/workflows/software/trimgalore.yml + - tests/software/trimgalore/** pull_request: paths: - software/trimgalore/** - - .github/workflows/trimgalore.yml - - tests + - .github/workflows/software/trimgalore.yml + - tests/software/trimgalore/** jobs: ci_test: